{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38122899", "kind": "science-record", "revision": 3, "content_hash": "sha256:1ca364d97d796d74e8844b0a15908b166a9bbea5030609f99c6d79706c3cdf6f", "created_at": "2026-11-01T19:20:03Z", "updated_at": "2026-11-01T22:10:54Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Interactome Analysis Reveals a Link of the Novel ALMS1-CEP70 Complex to Centrosomal Clusters.", "doi": "10.1016/j.mcpro.2023.100701", "pmid": "38122899", "authors": ["Franziska Woerz", "Felix Hoffmann", "Shibu Antony", "Sylvia Bolz", "Mohamed Ali Jarboui", "Katrin Junger", "Franziska Klose", "Isabel F Stehle", "Karsten Boldt", "Marius Ueffing", "Tina Beyer"], "journal": "Molecular & cellular proteomics : MCP", "year": 2024, "abstract": "Alström syndrome (ALMS) is a very rare autosomal-recessive disorder, causing a broad range of clinical defects most notably retinal degeneration, type 2 diabetes, and truncal obesity. The ALMS1 gene encodes a complex and huge ∼0.5 MDa protein, which has hampered analysis in the past. The ALMS1 protein is localized to the centrioles and the basal body of cilia and is involved in signaling processes, for example, TGF-β signaling. However, the exact molecular function of ALMS1 at the basal body remains elusive and controversial. We recently demonstrated that protein complex analysis utilizing endogenously tagged cells provides an excellent tool to investigate protein interactions of ciliary proteins. Here, CRISPR/Cas9-mediated endogenously tagged ALMS1 cells were used for affinity-based protein complex analysis. Centrosomal and microtubule-associated proteins were identified, which are potential regulators of ALMS1 function, such as the centrosomal protein 70 kDa (CEP70). Candidate proteins were further investigated in ALMS1-deficient hTERT-RPE1 cells. Loss of ALMS1 led to shortened cilia with no change in structural protein localization, for example, acetylated and ɣ-tubulin, Centrin-3, or the novel interactor CEP70. Conversely, reduction of CEP70 resulted in decreased ALMS1 at the ciliary basal body. Complex analysis of CEP70 revealed domain-specific ALMS1 interaction involving the TPR-containing C-terminal (TRP-CT) fragment of CEP70. In addition to ALMS1, several ciliary proteins, including CEP135, were found to specifically bind to the TPR-CT domain. Data are available via ProteomeXchange with the identifier PXD046401. Protein interactors identified in this study provide candidate lists that help to understand ALMS1 and CEP70 function in cilia-related protein modification, cell death, and disease-related mechanisms.", "claims": [{"id": "claim-method", "statement": "The Perseus software (version 1.6.14.0) was used for statistical analysis (17). Six biological replicates for each bait/tagged single clone and controls (RAF1 for CEP70, untagged cells for endogenously tagged ALMS1-sfGFP) are available for statistics. Potential contaminants and peptides only identified by side or reverse sequence were excluded for all data. Within the groups, a minimum half +1 of the samples should have valid values. Next, imputation by 0 was done for NaN values, the median values for each group followed by the ratio “specific bait/control” were calculated. Proteins which were significantly more abundant in one group were determined based on two statistical tests and classified in a two Tier system. Tier 1 interactors are stringently filtered with significance A (Benjamini-Hochberg FDR <0.05) and Student’s t test (Permutation-based FDR <0.05). Tier 2 includes additional proteins with a less stringent analysis (Significance A Benjamini Hochberg FDR <0.05 and Student’s t test p-value p < 0.05).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38122899", "locator": "sections[13] \"Experimental Design and Statistical Rationale\" paragraph 2", "quote": "The Perseus software (version 1.6.14.0) was used for statistical analysis (17). Six biological replicates for each bait/tagged single clone and controls (RAF1 for CEP70, untagged cells for endogenously tagged ALMS1-sfGFP) are available for statistics. Potential contaminants and peptides only identified by side or reverse sequence were excluded for all data. Within the groups, a minimum half +1 of the samples should have valid values. Next, imputation by 0 was done for NaN values, the median values for each group followed by the ratio “specific bait/control” were calculated. Proteins which were significantly more abundant in one group were determined based on two statistical tests and classified in a two Tier system. Tier 1 interactors are stringently filtered with significance A (Benjamini-Hochberg FDR <0.05) and Student’s t test (Permutation-based FDR <0.05). Tier 2 includes additional proteins with a less stringent analysis (Significance A Benjamini Hochberg FDR <0.05 and Student’s t test p-value p < 0.05)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD046401 (63).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38122899", "locator": "sections[26] \"Data Availability\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD046401 (63)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified CEP70 as an ALMS1 interactor and showed that CEP70 knockdown reduces ALMS1 at the ciliary basal body through interaction with the TPR-containing C-terminal domain of CEP70.", "kind": "quantitative", "target": {"value": 0.001, "unit": "p-value", "tolerance": null, "source": "Interestingly, CEP70 KD led to a very high significant reduction of ALMS1 intensity at the BB of cilia, indicating that CEP70 is involved in recruiting ALMS1 to or stabilization of ALMS1 at the BB (normalized intensity mean siCo = 212.9 ± 70.2 (89 cilia), normalized intensity mean siCEP70 = 132.9 ± 84.7 (56 cilia), p < 0.001; Fig. 5, C and D)."}, "evidence": [{"asset": "source:pmid:38122899", "locator": "sections[21] \"Complex Analysis Using Endogenously Tagged Cells Revealed New Interactions of ALMS1\" paragraph 5", "quote": "For the first time, CEP70 has been identified as an interaction partner of ALMS1."}, {"asset": "source:pmid:38122899", "locator": "sections[23] \"Loss of CEP70 led to Reduced ALMS1 at the Basal Body in hTERT-RPE1 Cells\" paragraph 4", "quote": "Interestingly, CEP70 KD led to a very high significant reduction of ALMS1 intensity at the BB of cilia, indicating that CEP70 is involved in recruiting ALMS1 to or stabilization of ALMS1 at the BB (normalized intensity mean siCo = 212.9 ± 70.2 (89 cilia), normalized intensity mean siCEP70 = 132.9 ± 84.7 (56 cilia), p < 0.001; Fig. 5, C and D)."}, {"asset": "source:pmid:38122899", "locator": "sections[24] \"CEP70 Interacts Domain Specific With ALMS1 and Other Centrosomal Proteins\" paragraph 6", "quote": "When analyzing the CEP70 fragments, ALMS1 was identified as a significant interactor in TPR-CT but not in CC1-2 hinting towards an ALMS1-independent localization of CEP70 to the BB (supplemental Fig. S6B)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The study identified CEP70 as an ALMS1 interactor and showed that CEP70 knockdown reduces ALMS1 at the ciliary basal body through interaction with the TPR-containing C-terminal domain of CEP70.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:38122899"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD046401"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD046401"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38122899", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.mcpro.2023.100701", "sha256": "sha256:69c8c0c7e3c7e6b3ba5669bb39ff2ad707c2f6a38d84a963726f88be8d8547aa", "bytes": 68476, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.mcpro.2023.100701", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10820798", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD046401", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD046401", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD046401", "version": null, "note": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD046401 (63).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD046401 (63).", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Interactome analysis reveals a link of the novel ALMS1-CEP70 complex to centrosomal clusters", "resolution_checked_at": "2026-11-01T19:09:50Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD046401 not downloaded", "asset:data:geo:PXD046401 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The Perseus software (version 1.6.14.0) was used for statistical analysis (17). Six biological replicates for each bait/tagged single clone and controls (RAF1 for CEP70, untagged cells for endogenously tagged ALMS1-sfGFP) are available for statistics. Potential contaminants and peptides only identified by side or reverse sequence were excluded for all data. Within the groups, a minimum half +1 of the samples should have valid values. Next, imputation by 0 was done for NaN values, the median values for each group followed by the ratio “specific bait/control” were calculated. Proteins which were significantly more abundant in one group were determined based on two statistical tests and classified in a two Tier system. Tier 1 interactors are stringently filtered with significance A (Benjamini-Hochberg FDR <0.05) and Student’s t test (Permutation-based FDR <0.05). Tier 2 includes additional proteins with a less stringent analysis (Significance A Benjamini Hochberg FDR <0.05 and Student’s t test p-value p < 0.05)."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": null, "expected_value": 0.001, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "gaps": ["method.student_t"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD046401"], "resolved_accessions": ["PXD046401"], "statements": ["The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD046401 (63)."], "basis": "The paper names PXD046401 in ProteomeXchange Consortium via the PRIDE partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:38122899", "data:geo:PXD046401"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD046401"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:03:06Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 20443, "completion_tokens": 1573, "cached_tokens": 256}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:38122899", "type": "paper", "label": "pmid:38122899"}, {"id": "source:pmid:38122899", "type": "manuscript", "label": "PMID 38122899 full text"}, {"id": "data:geo:PXD046401", "type": "dataset", "label": "GEO PXD046401"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38122899", "type": "paper", "label": "pmid:38122899"}, {"id": "source:pmid:38122899", "type": "manuscript", "label": "PMID 38122899 full text"}, {"id": "data:geo:PXD046401", "type": "dataset", "label": "GEO PXD046401"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38122899", "type": "extraction", "used": ["source:pmid:38122899"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD046401", "type": "accession_resolution", "used": ["data:geo:PXD046401"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:38122899", "parent_hash": "sha256:a2e669d0450d613b838fe2f3a1f9bf4016f9f0cbf2e70c80c281d0ff29be18cd", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:PXD046401 licence not read", "asset:data:geo:PXD046401 not downloaded", "execution.not_run", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "assays": [{"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.85, "evidence": ["tein interactions of ciliary proteins. Here, CRISPR/Cas9-mediated endogenously tagged ALMS1 cell"], "order_basis": "paper_text_order:762", "id": "assay:1"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["urther investigated in ALMS1-deficient hTERT-RPE1 cells. Loss of ALMS1 led to shortened cilia", "l Culture HEK293T (CRL-3216, ATCC) and hTERT-RPE1 (CRL-4000, ATCC) were grown in Dulbecco’s Mo"], "order_basis": "paper_text_order:1103", "id": "assay:2"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The Perseus software (version 1.6.14.0) was used for statistical analysis (17). Six biological replicates for each bait/tagged single clone and controls (RAF1 for CEP70, untagged cells for endogenously tagged ALMS1-sfGFP) are available for statistics. Potential contaminants and peptides only identified by side or reverse sequence were excluded for all data. Within the groups, a minimum half +1 of the samples should have valid values. Next, imputation by 0 was done for NaN values, the median values for each group followed by the ratio “specific bait/control” were calculated. Proteins which were significantly more abundant in one group were determined based on two statistical tests and classified in a two Tier system. Tier 1 interactors are stringently filtered with significance A (Benjamini-Hochberg FDR <0.05) and Student’s t test (Permutation-based FDR <0.05). Tier 2 includes additional proteins with a less stringent analysis (Significance A Benjamini Hochberg FDR <0.05 and Student’s t test p-value p < 0.05)."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T02:43:50+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}